Something I don't get

... and would appreciate an explanation, if one is available. The justice department reports to the executive branch, which is separate from the legislative and judicial branches. Legislative makes the laws, executive enforces them and judicial adjucates them.
Got that.
Congress can subpoena testimony and charge people with contempt and lying to congress. We had a valuable lesson in that 10 years ago.
However,
isn't it up to the justice department to charge and prosecute the people congress charges? If members of the president's administration get charged for lying to congress or refusing a subpoena, isn't it ultimately up to the president himself to have those charges enforced? Given that this whole thing is centered around the charge that the justice department was making political decisions, it seems likely the president would refuse to press charges against his administration.
I know Congress can chose to hold it's own trial on charges, but again, other than impeachment, is there anything they can do assuming a guilty verdict? Is there a congressional prison somewhere?(If so, I expected it is lavishly appointed and comes with franking privileges...)

Seems like the president holds the trump cards.

Edit: Some info from the heads at Volohk:
Congress has independent standing to seek a judicial order enforcing its subpoenas. They simply have a committee staff lawyer draft up a motion for an order to show cause and file it with the U.S. District Court for the District of Columbia. The Court will issue an order setting out a briefing and argument schedule, and it will go forward like any other case. Subpoena enforcement is not that hard, either in concept or execution.